X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=1b648fe1b8c4356bd7a3339240fb372353ceb3f6;hb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;hp=87c2739ca1a65ee17085b2b6924d523838b16503;hpb=196711de5050f77775a8df8f652ef6b36a88df2a;p=jalview.git
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 87c2739..1b648fe 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,598 +1,701 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package MCview;
-
-import javax.swing.*;
-import java.awt.event.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.gui.*;
-import jalview.io.EBIFetchClient;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
-
-public class PDBViewer extends JInternalFrame implements Runnable
-{
- PDBEntry pdb;
- Sequence sequence;
- PDBCanvas pdbcanvas;
-
-
- public PDBViewer(PDBEntry entry,
- Sequence seq,
- SeqCanvas seqcanvas)
- {
- /*Uncomment this to modify in Jbuilder
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }*/
-
- if (entry==null)
- return;
- pdb = entry;
- sequence = seq;
-
- Thread worker = new Thread(this);
- worker.start();
-
- pdbcanvas = new PDBCanvas(seqcanvas, seq);
-
- setContentPane(pdbcanvas);
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
- if(pdb.getProperty()!=null)
- {
- if (pdb.getProperty().get("method")!=null)
- {
- title.append(" Method: ");
- title.append(pdb.getProperty().get("method"));
- }
- if (pdb.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdb.getProperty().get("chains"));
- }
- }
- Desktop.addInternalFrame(this,title.toString(),400, 400);
- }
-
- public void run()
- {
- try
- {
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- String[] result = ebi.fetchData(query, "default","raw");
- if (result!=null) {
- PDBfile pdbfile = new PDBfile(result);
- pdbcanvas.setPDBFile(pdbfile);
- } else {
- throw new Exception("Empty result for WSDbFetch Query: "+query);
- }
-
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- showErrorMessage("Failed to retrieve PDB structure.");
-// this.dispose();
- }
- }
-
- private void jbInit()
- throws Exception
- {
- this.addKeyListener(new KeyAdapter()
- {
- public void keyPressed(KeyEvent evt)
- {
- pdbcanvas.keyPressed(evt);
- }
- });
-
- this.setJMenuBar(jMenuBar1);
- fileMenu.setText("File");
- coloursMenu.setText("Colours");
- saveMenu.setActionCommand("Save Image");
- saveMenu.setText("Save As");
- png.setText("PNG");
- png.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- png_actionPerformed(e);
- }
- });
- eps.setText("EPS");
- eps.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- eps_actionPerformed(e);
- }
- });
- mapping.setText("View Mapping");
- mapping.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- mapping_actionPerformed(e);
- }
- });
- wire.setText("Wireframe");
- wire.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- wire_actionPerformed(e);
- }
- });
- depth.setSelected(true);
- depth.setText("Depthcue");
- depth.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- depth_actionPerformed(e);
- }
- });
- zbuffer.setSelected(true);
- zbuffer.setText("Z Buffering");
- zbuffer.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zbuffer_actionPerformed(e);
- }
- });
- charge.setText("Charge & Cysteine");
- charge.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- charge_actionPerformed(e);
- }
- });
- chain.setText("By Chain");
- chain.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- chain_actionPerformed(e);
- }
- });
- seqButton.setSelected(true);
- seqButton.setText("By Sequence");
- seqButton.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- seqButton_actionPerformed(e);
- }
- });
- allchains.setSelected(true);
- allchains.setText("Show All Chains");
- allchains.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- allchains_itemStateChanged(e);
- }
- });
- zappo.setText("Zappo");
- zappo.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappo_actionPerformed(e);
- }
- });
- taylor.setText("Taylor");
- taylor.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylor_actionPerformed(e);
- }
- });
- hydro.setText("Hydro");
- hydro.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydro_actionPerformed(e);
- }
- });
- helix.setText("Helix");
- helix.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- helix_actionPerformed(e);
- }
- });
- strand.setText("Strand");
- strand.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- strand_actionPerformed(e);
- }
- });
- turn.setText("Turn");
- turn.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- turn_actionPerformed(e);
- }
- });
- buried.setText("Buried");
- buried.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- buried_actionPerformed(e);
- }
- });
- user.setText("User Defined...");
- user.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- user_actionPerformed(e);
- }
- });
- viewMenu.setText("View");
- background.setText("Background Colour...");
- background.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- background_actionPerformed(e);
- }
- });
- jMenuBar1.add(fileMenu);
- jMenuBar1.add(coloursMenu);
- jMenuBar1.add(viewMenu);
- fileMenu.add(saveMenu);
- fileMenu.add(mapping);
- saveMenu.add(png);
- saveMenu.add(eps);
- coloursMenu.add(seqButton);
- coloursMenu.add(chain);
- coloursMenu.add(charge);
- coloursMenu.add(zappo);
- coloursMenu.add(taylor);
- coloursMenu.add(hydro);
- coloursMenu.add(helix);
- coloursMenu.add(strand);
- coloursMenu.add(turn);
- coloursMenu.add(buried);
- coloursMenu.add(user);
- coloursMenu.add(background);
- ButtonGroup bg = new ButtonGroup();
- bg.add(seqButton);
- bg.add(chain);
- bg.add(charge);
- bg.add(zappo);
- bg.add(taylor);
- bg.add(hydro);
- bg.add(helix);
- bg.add(strand);
- bg.add(turn);
- bg.add(buried);
- bg.add(user);
-
-
- if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
- nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
- JOptionPane.YES_NO_OPTION);
- if(option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
- coloursMenu.remove(radioItem);
- }
- else
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- coloursMenu.add(radioItem);
- bg.add(radioItem);
- }
- }
-
- viewMenu.add(wire);
- viewMenu.add(depth);
- viewMenu.add(zbuffer);
- viewMenu.add(allchains);
- }
-
- JMenuBar jMenuBar1 = new JMenuBar();
- JMenu fileMenu = new JMenu();
- JMenu coloursMenu = new JMenu();
- JMenu saveMenu = new JMenu();
- JMenuItem png = new JMenuItem();
- JMenuItem eps = new JMenuItem();
- JMenuItem mapping = new JMenuItem();
- JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
- JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
- JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
- JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
-
- JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
- JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
- JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
- JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
- JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
- JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
- JRadioButtonMenuItem user = new JRadioButtonMenuItem();
- JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
- JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
- JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
- JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
- JMenu viewMenu = new JMenu();
- JMenuItem background = new JMenuItem();
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void eps_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.EPS);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.PNG);
- }
-
- void makePDBImage(int type)
- {
- int width = pdbcanvas.getWidth();
- int height = pdbcanvas.getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.PNG)
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.PNG,
- "Make PNG image from view",
- width, height,
- null, null);
- else
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.EPS,
- "Make EPS file from view",
- width, height,
- null, this.getTitle());
-
- if (im.getGraphics() != null)
- {
- pdbcanvas.drawAll(im.getGraphics(), width, height);
- im.writeImage();
- }
- }
- public void charge_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChargeColours();
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void hydro_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void chain_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChainColours();
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void zbuffer_actionPerformed(ActionEvent e)
- {
- pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void molecule_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void depth_actionPerformed(ActionEvent e)
- {
- pdbcanvas.depthcue = ! pdbcanvas.depthcue;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void wire_actionPerformed(ActionEvent e)
- {
- pdbcanvas.wire = ! pdbcanvas.wire;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void seqButton_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = true;
- pdbcanvas.updateSeqColours();
- }
-
-
- public void mapping_actionPerformed(ActionEvent e)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
- cap.setText(pdbcanvas.mappingDetails.toString());
- }
-
- public void allchains_itemStateChanged(ItemEvent e)
- {
- pdbcanvas.setAllchainsVisible(allchains.getState());
- }
- void showErrorMessage(String error)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
- }
-
-
- public void zappo_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new ZappoColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void taylor_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TaylorColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void helix_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HelixColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void strand_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new StrandColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void turn_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TurnColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void buried_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new BuriedColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void user_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals("User Defined..."))
- {
- new UserDefinedColours(pdbcanvas, null);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.
- getUserColourSchemes().get(e.getActionCommand());
-
- pdbcanvas.pdb.setColours(udc);
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
- }
-
- public void background_actionPerformed(ActionEvent e)
- {
- java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",
- pdbcanvas.backgroundColour);
-
- if(col!=null)
- {
- pdbcanvas.backgroundColour = col;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ */
+package MCview;
+
+import java.io.*;
+
+import java.awt.event.*;
+import javax.swing.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.ws.ebi.EBIFetchClient;
+
+import java.awt.BorderLayout;
+
+public class PDBViewer extends JInternalFrame implements Runnable
+{
+
+ /**
+ * The associated sequence in an alignment
+ */
+ PDBCanvas pdbcanvas;
+
+ PDBEntry pdbentry;
+
+ SequenceI[] seq;
+
+ String[] chains;
+
+ AlignmentPanel ap;
+
+ String protocol;
+
+ String tmpPDBFile;
+
+ public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+
+ {
+ this.pdbentry = pdbentry;
+ this.seq = seq;
+ this.chains = chains;
+ this.ap = ap;
+ this.protocol = protocol;
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+ + pdbentry.getFile());
+
+ pdbcanvas = new PDBCanvas();
+
+ setContentPane(pdbcanvas);
+
+ if (pdbentry.getFile() != null)
+ {
+ try
+ {
+ tmpPDBFile = pdbentry.getFile();
+ PDBfile pdbfile = new PDBfile(tmpPDBFile,
+ jalview.io.AppletFormatAdapter.FILE);
+
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ else
+ {
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ if (pdbentry.getProperty() != null)
+ {
+ if (pdbentry.getProperty().get("method") != null)
+ {
+ title.append(" Method: ");
+ title.append(pdbentry.getProperty().get("method"));
+ }
+ if (pdbentry.getProperty().get("chains") != null)
+ {
+ title.append(" Chain:");
+ title.append(pdbentry.getProperty().get("chains"));
+ }
+ }
+ Desktop.addInternalFrame(this, title.toString(), 400, 400);
+ }
+
+ public void run()
+ {
+ try
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ String query = "pdb:" + pdbentry.getId();
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+ .getAbsolutePath());
+
+ if (pdbentry.getFile() != null)
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+ } catch (Exception ex)
+ {
+ pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ this.addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ pdbcanvas.keyPressed(evt);
+ }
+ });
+
+ this.setJMenuBar(jMenuBar1);
+ fileMenu.setText("File");
+ coloursMenu.setText("Colours");
+ saveMenu.setActionCommand("Save Image");
+ saveMenu.setText("Save As");
+ png.setText("PNG");
+ png.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ png_actionPerformed(e);
+ }
+ });
+ eps.setText("EPS");
+ eps.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ eps_actionPerformed(e);
+ }
+ });
+ mapping.setText("View Mapping");
+ mapping.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ mapping_actionPerformed(e);
+ }
+ });
+ wire.setText("Wireframe");
+ wire.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ wire_actionPerformed(e);
+ }
+ });
+ depth.setSelected(true);
+ depth.setText("Depthcue");
+ depth.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ depth_actionPerformed(e);
+ }
+ });
+ zbuffer.setSelected(true);
+ zbuffer.setText("Z Buffering");
+ zbuffer.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zbuffer_actionPerformed(e);
+ }
+ });
+ charge.setText("Charge & Cysteine");
+ charge.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ charge_actionPerformed(e);
+ }
+ });
+ chain.setText("By Chain");
+ chain.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ chain_actionPerformed(e);
+ }
+ });
+ seqButton.setSelected(true);
+ seqButton.setText("By Sequence");
+ seqButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ seqButton_actionPerformed(e);
+ }
+ });
+ allchains.setSelected(true);
+ allchains.setText("Show All Chains");
+ allchains.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ allchains_itemStateChanged(e);
+ }
+ });
+ zappo.setText("Zappo");
+ zappo.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappo_actionPerformed(e);
+ }
+ });
+ taylor.setText("Taylor");
+ taylor.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylor_actionPerformed(e);
+ }
+ });
+ hydro.setText("Hydro");
+ hydro.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydro_actionPerformed(e);
+ }
+ });
+ helix.setText("Helix");
+ helix.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helix_actionPerformed(e);
+ }
+ });
+ strand.setText("Strand");
+ strand.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strand_actionPerformed(e);
+ }
+ });
+ turn.setText("Turn");
+ turn.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turn_actionPerformed(e);
+ }
+ });
+ buried.setText("Buried");
+ buried.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buried_actionPerformed(e);
+ }
+ });
+ user.setText("User Defined...");
+ user.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ user_actionPerformed(e);
+ }
+ });
+ viewMenu.setText("View");
+ background.setText("Background Colour...");
+ background.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ background_actionPerformed(e);
+ }
+ });
+ savePDB.setText("PDB File");
+ savePDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ savePDB_actionPerformed(e);
+ }
+ });
+ jMenuBar1.add(fileMenu);
+ jMenuBar1.add(coloursMenu);
+ jMenuBar1.add(viewMenu);
+ fileMenu.add(saveMenu);
+ fileMenu.add(mapping);
+ saveMenu.add(savePDB);
+ saveMenu.add(png);
+ saveMenu.add(eps);
+ coloursMenu.add(seqButton);
+ coloursMenu.add(chain);
+ coloursMenu.add(charge);
+ coloursMenu.add(zappo);
+ coloursMenu.add(taylor);
+ coloursMenu.add(hydro);
+ coloursMenu.add(helix);
+ coloursMenu.add(strand);
+ coloursMenu.add(turn);
+ coloursMenu.add(buried);
+ coloursMenu.add(user);
+ coloursMenu.add(background);
+ ButtonGroup bg = new ButtonGroup();
+ bg.add(seqButton);
+ bg.add(chain);
+ bg.add(charge);
+ bg.add(zappo);
+ bg.add(taylor);
+ bg.add(hydro);
+ bg.add(helix);
+ bg.add(strand);
+ bg.add(turn);
+ bg.add(buried);
+ bg.add(user);
+
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColours.nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ coloursMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ user_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ user_actionPerformed(evt);
+ }
+ });
+ coloursMenu.add(radioItem);
+ bg.add(radioItem);
+ }
+ }
+
+ viewMenu.add(wire);
+ viewMenu.add(depth);
+ viewMenu.add(zbuffer);
+ viewMenu.add(allchains);
+ }
+
+ JMenuBar jMenuBar1 = new JMenuBar();
+
+ JMenu fileMenu = new JMenu();
+
+ JMenu coloursMenu = new JMenu();
+
+ JMenu saveMenu = new JMenu();
+
+ JMenuItem png = new JMenuItem();
+
+ JMenuItem eps = new JMenuItem();
+
+ JMenuItem mapping = new JMenuItem();
+
+ JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
+
+ JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem user = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
+
+ JMenu viewMenu = new JMenu();
+
+ JMenuItem background = new JMenuItem();
+
+ JMenuItem savePDB = new JMenuItem();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.EPS);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.PNG);
+ }
+
+ void makePDBImage(int type)
+ {
+ int width = pdbcanvas.getWidth();
+ int height = pdbcanvas.getHeight();
+
+ jalview.util.ImageMaker im;
+
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ "Make PNG image from view", width, height, null, null);
+ }
+ else
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Make EPS file from view", width, height, null,
+ this.getTitle());
+ }
+
+ if (im.getGraphics() != null)
+ {
+ pdbcanvas.drawAll(im.getGraphics(), width, height);
+ im.writeImage();
+ }
+ }
+
+ public void charge_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChargeColours();
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void hydro_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void chain_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChainColours();
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void zbuffer_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void molecule_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void depth_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.depthcue = !pdbcanvas.depthcue;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void wire_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.wire = !pdbcanvas.wire;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void seqButton_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = true;
+ pdbcanvas.updateSeqColours();
+ }
+
+ public void mapping_actionPerformed(ActionEvent e)
+ {
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ try
+ {
+ cap.setText(pdbcanvas.mappingDetails.toString());
+ Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Opening sequence to structure mapping report", oom);
+ cap.dispose();
+ }
+ }
+
+ public void allchains_itemStateChanged(ItemEvent e)
+ {
+ pdbcanvas.setAllchainsVisible(allchains.getState());
+ }
+
+ public void zappo_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new ZappoColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void taylor_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new TaylorColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void helix_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new HelixColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void strand_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new StrandColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void turn_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new TurnColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void buried_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new BuriedColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void user_actionPerformed(ActionEvent e)
+ {
+ if (e.getActionCommand().equals("User Defined..."))
+ {
+ // new UserDefinedColours(pdbcanvas, null);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
+
+ pdbcanvas.pdb.setColours(udc);
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+ }
+
+ public void background_actionPerformed(ActionEvent e)
+ {
+ java.awt.Color col = JColorChooser.showDialog(this,
+ "Select Background Colour", pdbcanvas.backgroundColour);
+
+ if (col != null)
+ {
+ pdbcanvas.backgroundColour = col;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+ }
+
+ public void savePDB_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save PDB File");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("") > -1 || data.indexOf("") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+}